On Thu, Jun 14, 2012 at 12:07 PM, MH <[email protected]> wrote: > 1) I have been working from your page. > http://aroma-project.org/vignettes/CalMaTe - over the course of the last > couple of days. I have been following that carefully..
> On Thu, Jun 14, 2012 at 12:59 PM, MH <[email protected]> wrote: >> More or less the complete script follows.. >> >> dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose); >> print(dsList); >> >> cmt <- CalMaTeCalibration(dsList); >> print(cmt); >> >> >> sampleName <- "2_S7_CD15_SNP6"; >> >> >> patientIDs <- c(1,2,4); >> sampleTypes <- c("tumor", "normal"); >> >> pids <- rep(patientIDs, each=length(sampleTypes)); >> types <- rep(sampleTypes, times=length(patientIDs)); >> >> mat <- cbind(names, pids, types); >> str(mat); >> >> idxsN <- which(mat[, "types"] == "normal"); >> >> >> cmtN <- CalMaTeCalibration(dsList, tags=c("*", "normalReferences"), >> references=idxsN); > > 2) > print(cmtN); > CalMaTeCalibration: > Data sets (2): > <Total>: > AromaUnitTotalCnBinarySet: > Name: CLLtest > Tags: ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > Full name: CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > Number of files: 6 > Names: 1_S7_CD3_SNP6, 2_S7_CD15_SNP6, 3_S7_CD19_SNP6, ..., 6_S29_CD19_SNP6 > [6] > Path (to the first file): > totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6 > Total file size: 43.06 MB > RAM: 0.01MB > <FracB>: > AromaUnitFracBCnBinarySet: > Name: CLLtest > Tags: ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > Full name: CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY > Number of files: 6 > Names: 1_S7_CD3_SNP6, 2_S7_CD15_SNP6, 3_S7_CD19_SNP6, ..., 6_S29_CD19_SNP6 > [6] > Path (to the first file): > totalAndFracBData/CLLtest,ACC,ra,-XY,BPN,-XY,RMA,FLN,-XY/GenomeWideSNP_6 > Total file size: 43.06 MB > RAM: 0.00MB > Number of arrays: 6 > Number of references: 3 (50.00%) > Additional parameters: [2] references: int [1:3] 2 4 6, flavor: chr "v2" > > 3) > sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] preprocessCore_1.16.0 BiocInstaller_1.2.1 sfit_0.1.9 > calmate_0.9.2 > [5] MASS_7.3-17 aroma.affymetrix_2.5.0 affxparser_1.26.4 > aroma.apd_0.2.2 > [9] R.huge_0.3.0 aroma.core_2.5.0 aroma.light_1.24.0 > matrixStats_0.5.0 > [13] R.rsp_0.7.5 R.cache_0.6.2 R.filesets_1.1.5 > digest_0.5.2 > [17] R.utils_1.12.1 R.oo_1.9.3 R.methodsS3_1.2.2 > > loaded via a namespace (and not attached): > [1] splines_2.14.2 tools_2.14.2 All of the above looks good. FYI, all methods of the Aroma framework are designed to use a constant amount of memory regardless of chip type and number of samples, so it's a bit weird that you "run out of memory" (or more likely, the memory allocated for/by R is so fragmented that it cannot allocate a continuous stretch of 95.4 Mbytes). Also, the above script is run part of the regular system tests and there we don't run out of memory, but I'll check the memory usage on my Windows 7 machine when I have time. Regardless, I don't think it is possible troubleshoot this further. The good thing though, you can just restart with a fresh R session, rerun your script and things should go well. Since aroma stores intermediate and final results to the file system, any steps that have already been processed will already be there so it should be really quick to rerun it. Let us know if that works. Best, Henrik > > thanks, M > > > On Thursday, June 14, 2012 2:31:02 PM UTC-4, Henrik Bengtsson wrote: >> >> >> > Hi All, >> > I have my test run almost completed and at the step >> > dsCNList <- process(cmtN, verbose=verbose); >> > I get the following memory error >> > Error: cannot allocate vector of size 95.4 Mb >> > >> > I am on Windows7, 32bit and have many Gs of storage. >> > >> > Any ideas for how to deal with this? >> >> My best guess now is that you have done lots of other things in the >> same R session before doing your aroma analysis, but it is impossible >> to tell based on that single line of code. So, please post (1) your >> complete script (at least up to the point where you get the error), >> (2) the output of print(cmtN), (3) the output of sessionInfo() after >> you get the error. >> >> /Henrik >> >> > thanks, M >> > >> > -- >> > When reporting problems on aroma.affymetrix, make sure 1) to run the >> > latest >> > version of the package, 2) to report the output of sessionInfo() and >> > traceback(), and 3) to post a complete code example. >> > >> > >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group with website http://www.aroma-project.org/. >> > To post to this group, send email to [email protected] >> > To unsubscribe and other options, go to >> > http://www.aroma-project.org/forum/ > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to [email protected] > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
